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The BAT (Biclustering Analysis ToolBox) is a user-friendly software toolbox which implements the BiHEA algorithm together with several means for visualization and biclustering analysis. The main facilities of the BAT can be summarized as follows:

Data handling.

All data, being the entire expression matrix loaded from an external file or sets of biclusters, are organized in a list structure that is depicted in the left panel of the graphical user interface. All the work performed with the software can be saved as a project form and restored later.

Data pre-processing.

The input data file can be any CSV file including annotations of genes and conditions. The loaded gene expression data can then be transformed by means of translation, escalation or standardization.


The expression matrix can be displayed as a heatmap or as a numerical matrix. Annotations of the conditions run along the top whereas the annotations of the genes are listed on the left hand side. Biclusters can be visualized in three different ways: in the form of a heatmap, a numerical sub-matrix, or as a collection of gene expression profiles.


For further investigations, the software offers the possibility of a gene pair analysis. In particular, for each pair of genes it is calculated how often these genes occur together in the same bicluster. This number of co-occurrence indicates which genes may be functionally related. Additionally, the degree of coverage of the resulting biclusters with respect to the gene expression matrix can be visualized as a grey scale matrix.

All the figures, graphs, and results can be exported for further usages on presentations, papers, etc.

In order to download the software, please login. It is free!